Current mRNA (e.g., gene expression based) prognostic breast cancer screening tests (such as Oncotype DX) assay for expression of a limited number of unrelated genes, each known to be involved in breast cancer progression. Because breast cancer is a very heterogeneous disease, these tests fail to select those patients who are most likely to benefit from a given targeted therapy, including a rapidly growing list of existing and new drugs. Thus, health care providers are forced to try random combinations of available drugs in hopes that these combination treatments will provide a clinical response or clinical benefit. These strategies also fail to link expression of any collection of gene expression data to any defined mechanism(s) responsible for their expression (i.e., the targets are unknown).